## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic Transcript dynamics (TSS ~ TES)

Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)

When counting with either adapters, the clustering grouped ORF64 together with two late genes

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1    ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1    ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1    ORF9 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1   ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       1   ORF37 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14:       1   ORF49 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16:       1   ORF51 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17:       1   ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19:       1   ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20:       1  NOIR_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 21:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 22:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 23:       1   ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 24:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 25:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31:       2   ORF22 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32:       2   ORF23 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33:       2   ORF24 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 34:       2   ORF25 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 35:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 36:       2   ORF27 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 37:       2   ORF28 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 38:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 39:       2   ORF32 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 40:       2   ORF33 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 41:       2 ORF35.5 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 42:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 43:       2   ORF39 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 44:       2     CTO 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 45:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 46:       2   ORF42 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 47:       2   ORF43 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 48:       2   ORF44 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 49:       2   ORF46 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 50:       2   ORF58 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 51:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 52:       2   ORF62 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 53:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 54:       2   ORF68 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 55:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 56:       2   ORF74 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 57:       2   ORF75 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 58:       2   ORF76 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 59:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 60:       4    ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 61:       4   ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 62:       4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 63:       4   ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 64:       5   ORF12 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 65:       5   ORF13 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 66:       5   ORF15 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 67:       5   ORF16 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 68:       5   ORF35 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 69:       5   ORF41 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 70:       5   ORF48 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 71:       5   ORF52 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 72:       5   ORF54 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 73:       5   ORF57 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 74:       5   ORF60 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 75:       5   ORF71 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 76:       5   ORF72 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001626964 -3.0659483 0.9195982 0.57648065
## 21: 0.001626964 -3.0659483 0.9195982 0.57648065
## 22: 0.001626964 -3.0659483 0.9195982 0.57648065
## 23: 0.001626964 -3.0659483 0.9195982 0.57648065
## 24: 0.001626964 -3.0659483 0.9195982 0.57648065
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.001864476 -3.0095246 0.9788818 0.61510585
## 34: 0.001864476 -3.0095246 0.9788818 0.61510585
## 35: 0.001864476 -3.0095246 0.9788818 0.61510585
## 36: 0.001864476 -3.0095246 0.9788818 0.61510585
## 37: 0.001864476 -3.0095246 0.9788818 0.61510585
## 38: 0.001864476 -3.0095246 0.9788818 0.61510585
## 39: 0.001864476 -3.0095246 0.9788818 0.61510585
## 40: 0.001864476 -3.0095246 0.9788818 0.61510585
## 41: 0.001864476 -3.0095246 0.9788818 0.61510585
## 42: 0.001864476 -3.0095246 0.9788818 0.61510585
## 43: 0.001864476 -3.0095246 0.9788818 0.61510585
## 44: 0.001864476 -3.0095246 0.9788818 0.61510585
## 45: 0.001864476 -3.0095246 0.9788818 0.61510585
## 46: 0.001864476 -3.0095246 0.9788818 0.61510585
## 47: 0.001864476 -3.0095246 0.9788818 0.61510585
## 48: 0.001864476 -3.0095246 0.9788818 0.61510585
## 49: 0.001864476 -3.0095246 0.9788818 0.61510585
## 50: 0.001864476 -3.0095246 0.9788818 0.61510585
## 51: 0.001864476 -3.0095246 0.9788818 0.61510585
## 52: 0.001864476 -3.0095246 0.9788818 0.61510585
## 53: 0.001864476 -3.0095246 0.9788818 0.61510585
## 54: 0.001864476 -3.0095246 0.9788818 0.61510585
## 55: 0.001864476 -3.0095246 0.9788818 0.61510585
## 56: 0.001864476 -3.0095246 0.9788818 0.61510585
## 57: 0.001864476 -3.0095246 0.9788818 0.61510585
## 58: 0.001864476 -3.0095246 0.9788818 0.61510585
## 59: 0.003563035 -2.1172717 0.8723685 0.47463144
## 60: 0.001370130 -3.1781458 0.9289840 0.55960768
## 61: 0.001370130 -3.1781458 0.9289840 0.55960768
## 62: 0.001370130 -3.1781458 0.9289840 0.55960768
## 63: 0.001370130 -3.1781458 0.9289840 0.55960768
## 64: 0.005277101 -0.7191323 0.5947468 0.03730409
## 65: 0.005277101 -0.7191323 0.5947468 0.03730409
## 66: 0.005277101 -0.7191323 0.5947468 0.03730409
## 67: 0.005277101 -0.7191323 0.5947468 0.03730409
## 68: 0.005277101 -0.7191323 0.5947468 0.03730409
## 69: 0.005277101 -0.7191323 0.5947468 0.03730409
## 70: 0.005277101 -0.7191323 0.5947468 0.03730409
## 71: 0.005277101 -0.7191323 0.5947468 0.03730409
## 72: 0.005277101 -0.7191323 0.5947468 0.03730409
## 73: 0.005277101 -0.7191323 0.5947468 0.03730409
## 74: 0.005277101 -0.7191323 0.5947468 0.03730409
## 75: 0.005277101 -0.7191323 0.5947468 0.03730409
## 76: 0.005277101 -0.7191323 0.5947468 0.03730409
##           se.bp          v         c       pchi

## [1] "ORF37" "ORF49" "ORF58" "ORF27" "ORF42" "ORF33" "ORF62"
## [1] 7
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 13

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1    ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1    ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1   ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13:       1   ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15:       1   ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18:       1   ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26:       2   ORF22 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27:       2   ORF23 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28:       2   ORF24 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29:       2   ORF25 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31:       2   ORF27 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32:       2   ORF28 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 34:       2   ORF32 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 35:       2   ORF33 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 36:       2 ORF35.5 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 37:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 38:       2   ORF39 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 39:       2     CTO 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 40:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 41:       2   ORF42 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 42:       2   ORF43 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 43:       2   ORF44 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 44:       2   ORF46 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 45:       2   ORF58 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 46:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 47:       2   ORF62 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 48:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 49:       2   ORF68 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 50:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 51:       2   ORF74 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 52:       2   ORF75 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 53:       2   ORF76 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 54:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 55:       4    ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 56:       4   ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 57:       4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 58:       4   ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 59:       5    ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 60:       5   ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 61:       5   ORF49 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 62:       5   ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 63:       5  NOIR_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 64:       6   ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 65:       6   ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 66:       6   ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 67:       6   ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 68:       6   ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 69:       6   ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 70:       6   ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 71:       6   ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 72:       6   ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 73:       6   ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 74:       6   ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 75:       6   ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 76:       6   ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.001864476 -3.0095246 0.9788818 0.61510585
## 34: 0.001864476 -3.0095246 0.9788818 0.61510585
## 35: 0.001864476 -3.0095246 0.9788818 0.61510585
## 36: 0.001864476 -3.0095246 0.9788818 0.61510585
## 37: 0.001864476 -3.0095246 0.9788818 0.61510585
## 38: 0.001864476 -3.0095246 0.9788818 0.61510585
## 39: 0.001864476 -3.0095246 0.9788818 0.61510585
## 40: 0.001864476 -3.0095246 0.9788818 0.61510585
## 41: 0.001864476 -3.0095246 0.9788818 0.61510585
## 42: 0.001864476 -3.0095246 0.9788818 0.61510585
## 43: 0.001864476 -3.0095246 0.9788818 0.61510585
## 44: 0.001864476 -3.0095246 0.9788818 0.61510585
## 45: 0.001864476 -3.0095246 0.9788818 0.61510585
## 46: 0.001864476 -3.0095246 0.9788818 0.61510585
## 47: 0.001864476 -3.0095246 0.9788818 0.61510585
## 48: 0.001864476 -3.0095246 0.9788818 0.61510585
## 49: 0.001864476 -3.0095246 0.9788818 0.61510585
## 50: 0.001864476 -3.0095246 0.9788818 0.61510585
## 51: 0.001864476 -3.0095246 0.9788818 0.61510585
## 52: 0.001864476 -3.0095246 0.9788818 0.61510585
## 53: 0.001864476 -3.0095246 0.9788818 0.61510585
## 54: 0.003563035 -2.1172717 0.8723685 0.47463144
## 55: 0.001370130 -3.1781458 0.9289840 0.55960768
## 56: 0.001370130 -3.1781458 0.9289840 0.55960768
## 57: 0.001370130 -3.1781458 0.9289840 0.55960768
## 58: 0.001370130 -3.1781458 0.9289840 0.55960768
## 59: 0.005277101 -0.7191323 0.5947468 0.03730409
## 60: 0.005277101 -0.7191323 0.5947468 0.03730409
## 61: 0.005277101 -0.7191323 0.5947468 0.03730409
## 62: 0.005277101 -0.7191323 0.5947468 0.03730409
## 63: 0.005277101 -0.7191323 0.5947468 0.03730409
## 64: 0.005289339 -1.7163469 1.3494170 0.51125155
## 65: 0.005289339 -1.7163469 1.3494170 0.51125155
## 66: 0.005289339 -1.7163469 1.3494170 0.51125155
## 67: 0.005289339 -1.7163469 1.3494170 0.51125155
## 68: 0.005289339 -1.7163469 1.3494170 0.51125155
## 69: 0.005289339 -1.7163469 1.3494170 0.51125155
## 70: 0.005289339 -1.7163469 1.3494170 0.51125155
## 71: 0.005289339 -1.7163469 1.3494170 0.51125155
## 72: 0.005289339 -1.7163469 1.3494170 0.51125155
## 73: 0.005289339 -1.7163469 1.3494170 0.51125155
## 74: 0.005289339 -1.7163469 1.3494170 0.51125155
## 75: 0.005289339 -1.7163469 1.3494170 0.51125155
## 76: 0.005289339 -1.7163469 1.3494170 0.51125155
##           se.bp          v         c       pchi

## [1] "ORF38" "ORF58" "ORF27" "ORF42" "ORF33" "ORF62" "ORF49"
## [1] 7
## [1] "ORF9"   "ORF37"  "ORF49"  "ORF51"  "NOIR_1"
## [1] 5

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1    ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1    ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1   ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13:       1   ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15:       1   ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18:       1   ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 34:       4    ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 35:       4   ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 36:       4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 37:       4   ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 38:       5    ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 39:       5   ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 40:       5   ORF49 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 41:       5   ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 42:       5  NOIR_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 43:       6   ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 44:       6   ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 45:       6   ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 46:       6   ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 47:       6   ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 48:       6   ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 49:       6   ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 50:       6   ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 51:       6   ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 52:       6   ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 53:       6   ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 54:       6   ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 55:       6   ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 56:       7   ORF22 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 57:       7   ORF23 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 58:       7   ORF24 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 59:       7   ORF25 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 60:       7   ORF27 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 61:       7   ORF28 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 62:       7   ORF32 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 63:       7   ORF33 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 64:       7 ORF35.5 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 65:       7   ORF39 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 66:       7     CTO 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 67:       7   ORF42 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 68:       7   ORF43 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 69:       7   ORF44 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 70:       7   ORF46 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 71:       7   ORF58 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 72:       7   ORF62 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 73:       7   ORF68 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 74:       7   ORF74 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 75:       7   ORF75 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 76:       7   ORF76 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.003563035 -2.1172717 0.8723685 0.47463144
## 34: 0.001370130 -3.1781458 0.9289840 0.55960768
## 35: 0.001370130 -3.1781458 0.9289840 0.55960768
## 36: 0.001370130 -3.1781458 0.9289840 0.55960768
## 37: 0.001370130 -3.1781458 0.9289840 0.55960768
## 38: 0.005277101 -0.7191323 0.5947468 0.03730409
## 39: 0.005277101 -0.7191323 0.5947468 0.03730409
## 40: 0.005277101 -0.7191323 0.5947468 0.03730409
## 41: 0.005277101 -0.7191323 0.5947468 0.03730409
## 42: 0.005277101 -0.7191323 0.5947468 0.03730409
## 43: 0.005289339 -1.7163469 1.3494170 0.51125155
## 44: 0.005289339 -1.7163469 1.3494170 0.51125155
## 45: 0.005289339 -1.7163469 1.3494170 0.51125155
## 46: 0.005289339 -1.7163469 1.3494170 0.51125155
## 47: 0.005289339 -1.7163469 1.3494170 0.51125155
## 48: 0.005289339 -1.7163469 1.3494170 0.51125155
## 49: 0.005289339 -1.7163469 1.3494170 0.51125155
## 50: 0.005289339 -1.7163469 1.3494170 0.51125155
## 51: 0.005289339 -1.7163469 1.3494170 0.51125155
## 52: 0.005289339 -1.7163469 1.3494170 0.51125155
## 53: 0.005289339 -1.7163469 1.3494170 0.51125155
## 54: 0.005289339 -1.7163469 1.3494170 0.51125155
## 55: 0.005289339 -1.7163469 1.3494170 0.51125155
## 56: 0.005184396 -0.5512413 0.7915023 0.13830228
## 57: 0.005184396 -0.5512413 0.7915023 0.13830228
## 58: 0.005184396 -0.5512413 0.7915023 0.13830228
## 59: 0.005184396 -0.5512413 0.7915023 0.13830228
## 60: 0.005184396 -0.5512413 0.7915023 0.13830228
## 61: 0.005184396 -0.5512413 0.7915023 0.13830228
## 62: 0.005184396 -0.5512413 0.7915023 0.13830228
## 63: 0.005184396 -0.5512413 0.7915023 0.13830228
## 64: 0.005184396 -0.5512413 0.7915023 0.13830228
## 65: 0.005184396 -0.5512413 0.7915023 0.13830228
## 66: 0.005184396 -0.5512413 0.7915023 0.13830228
## 67: 0.005184396 -0.5512413 0.7915023 0.13830228
## 68: 0.005184396 -0.5512413 0.7915023 0.13830228
## 69: 0.005184396 -0.5512413 0.7915023 0.13830228
## 70: 0.005184396 -0.5512413 0.7915023 0.13830228
## 71: 0.005184396 -0.5512413 0.7915023 0.13830228
## 72: 0.005184396 -0.5512413 0.7915023 0.13830228
## 73: 0.005184396 -0.5512413 0.7915023 0.13830228
## 74: 0.005184396 -0.5512413 0.7915023 0.13830228
## 75: 0.005184396 -0.5512413 0.7915023 0.13830228
## 76: 0.005184396 -0.5512413 0.7915023 0.13830228
##           se.bp          v         c       pchi

##  [1] "ORF38" "ORF49" "ORF75" "ORF23" "ORF74" "ORF58" "ORF27" "ORF32" "ORF42"
## [10] "ORF68" "ORF39" "ORF22" "ORF28" "ORF33" "CTO"   "ORF76" "ORF62"
## [1] 17
##  [1] "ORF9"    "ORF37"   "ORF49"   "ORF51"   "NOIR_1"  "ORF22"   "ORF23"  
##  [8] "ORF24"   "ORF25"   "ORF27"   "ORF28"   "ORF32"   "ORF33"   "ORF35.5"
## [15] "ORF39"   "CTO"     "ORF42"   "ORF43"   "ORF44"   "ORF46"   "ORF58"  
## [22] "ORF62"   "ORF68"   "ORF74"   "ORF75"   "ORF76"
## [1] 26

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1    ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1    ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1   ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13:       1   ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15:       1   ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18:       1   ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 34:       4    ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 35:       4   ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 36:       4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 37:       4   ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 38:       5    ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 39:       5   ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 40:       5   ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 41:       6   ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 42:       6   ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 43:       6   ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 44:       6   ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 45:       6   ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 46:       6   ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 47:       6   ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 48:       6   ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 49:       6   ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 50:       6   ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 51:       6   ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 52:       6   ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 53:       6   ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 54:       7   ORF22 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 55:       7   ORF23 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 56:       7   ORF25 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 57:       7   ORF28 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 58:       7   ORF33 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 59:       7 ORF35.5 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 60:       7   ORF39 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 61:       7     CTO 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 62:       7   ORF42 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 63:       7   ORF43 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 64:       7   ORF44 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 65:       7   ORF46 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 66:       7   ORF58 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 67:       7   ORF62 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 68:       7   ORF68 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 69:       7   ORF75 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 70:       8   ORF24 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 71:       8   ORF74 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 72:       8   ORF76 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 73:       9   ORF27 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 74:       9   ORF32 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 75:      10   ORF49 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 76:      10  NOIR_1 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.003563035 -2.1172717 0.8723685 0.47463144
## 34: 0.001370130 -3.1781458 0.9289840 0.55960768
## 35: 0.001370130 -3.1781458 0.9289840 0.55960768
## 36: 0.001370130 -3.1781458 0.9289840 0.55960768
## 37: 0.001370130 -3.1781458 0.9289840 0.55960768
## 38: 0.005277101 -0.7191323 0.5947468 0.03730409
## 39: 0.005277101 -0.7191323 0.5947468 0.03730409
## 40: 0.005277101 -0.7191323 0.5947468 0.03730409
## 41: 0.005289339 -1.7163469 1.3494170 0.51125155
## 42: 0.005289339 -1.7163469 1.3494170 0.51125155
## 43: 0.005289339 -1.7163469 1.3494170 0.51125155
## 44: 0.005289339 -1.7163469 1.3494170 0.51125155
## 45: 0.005289339 -1.7163469 1.3494170 0.51125155
## 46: 0.005289339 -1.7163469 1.3494170 0.51125155
## 47: 0.005289339 -1.7163469 1.3494170 0.51125155
## 48: 0.005289339 -1.7163469 1.3494170 0.51125155
## 49: 0.005289339 -1.7163469 1.3494170 0.51125155
## 50: 0.005289339 -1.7163469 1.3494170 0.51125155
## 51: 0.005289339 -1.7163469 1.3494170 0.51125155
## 52: 0.005289339 -1.7163469 1.3494170 0.51125155
## 53: 0.005289339 -1.7163469 1.3494170 0.51125155
## 54: 0.005184396 -0.5512413 0.7915023 0.13830228
## 55: 0.005184396 -0.5512413 0.7915023 0.13830228
## 56: 0.005184396 -0.5512413 0.7915023 0.13830228
## 57: 0.005184396 -0.5512413 0.7915023 0.13830228
## 58: 0.005184396 -0.5512413 0.7915023 0.13830228
## 59: 0.005184396 -0.5512413 0.7915023 0.13830228
## 60: 0.005184396 -0.5512413 0.7915023 0.13830228
## 61: 0.005184396 -0.5512413 0.7915023 0.13830228
## 62: 0.005184396 -0.5512413 0.7915023 0.13830228
## 63: 0.005184396 -0.5512413 0.7915023 0.13830228
## 64: 0.005184396 -0.5512413 0.7915023 0.13830228
## 65: 0.005184396 -0.5512413 0.7915023 0.13830228
## 66: 0.005184396 -0.5512413 0.7915023 0.13830228
## 67: 0.005184396 -0.5512413 0.7915023 0.13830228
## 68: 0.005184396 -0.5512413 0.7915023 0.13830228
## 69: 0.005184396 -0.5512413 0.7915023 0.13830228
## 70: 0.005314391 -0.9727072 0.8743440 0.26787994
## 71: 0.005314391 -0.9727072 0.8743440 0.26787994
## 72: 0.005314391 -0.9727072 0.8743440 0.26787994
## 73: 0.005288858 -0.8567880 0.7295011 0.03771967
## 74: 0.005288858 -0.8567880 0.7295011 0.03771967
## 75: 0.005328329 -0.9683955 0.9780811 0.28653102
## 76: 0.005328329 -0.9683955 0.9780811 0.28653102
##           se.bp          v         c       pchi

## [1] "ORF38" "ORF62" "ORF28" "ORF68" "ORF76" "ORF49"
## [1] 6
##  [1] "ORF9"    "ORF37"   "ORF51"   "ORF22"   "ORF23"   "ORF25"   "ORF28"  
##  [8] "ORF33"   "ORF35.5" "ORF39"   "CTO"     "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF58"   "ORF62"   "ORF68"   "ORF75"   "ORF27"   "ORF32"
## [1] 21

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 13:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 14:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 15:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 16:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 17:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 18:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 19:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 20:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 26:       4    ORF5 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 27:       4    ORF7 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 28:       4   ORF10 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 29:       4   ORF17 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 30:       4   ORF30 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 31:       4   ORF53 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 32:       4   ORF63 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 33:       4   ORF69 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 34:       5    ORF6 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 35:       5   ORF18 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 36:       5 ORF64_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 37:       6    ORF9 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 38:       6   ORF37 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 39:       6   ORF51 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 40:       7   ORF12 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 41:       7   ORF13 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 42:       7   ORF15 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 43:       7   ORF16 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 44:       7   ORF35 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 45:       7   ORF41 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 46:       7   ORF48 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 47:       7   ORF52 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 48:       7   ORF54 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 49:       7   ORF57 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 50:       7   ORF60 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 51:       7   ORF71 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 52:       7   ORF72 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 53:       8   ORF22 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 54:       8   ORF23 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 55:       8   ORF25 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 56:       8   ORF28 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 57:       8   ORF33 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 58:       8 ORF35.5 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 59:       8   ORF39 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 60:       8     CTO 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 61:       8   ORF42 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 62:       8   ORF43 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 63:       8   ORF44 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 64:       8   ORF46 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 65:       8   ORF58 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 66:       8   ORF62 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 67:       8   ORF68 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 68:       8   ORF75 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 69:       9   ORF24 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 70:       9   ORF74 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 71:       9   ORF76 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 72:      10   ORF27 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 73:      10   ORF32 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 74:      11   ORF49 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 75:      11  NOIR_1 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 76:      12   ORF70 0.9815714 0.9979697 0.6635465 3.593511e-03 5.276070e-04
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001864476 -3.0095246 0.9788818 0.61510585
## 13: 0.001864476 -3.0095246 0.9788818 0.61510585
## 14: 0.001864476 -3.0095246 0.9788818 0.61510585
## 15: 0.001864476 -3.0095246 0.9788818 0.61510585
## 16: 0.001864476 -3.0095246 0.9788818 0.61510585
## 17: 0.001864476 -3.0095246 0.9788818 0.61510585
## 18: 0.001864476 -3.0095246 0.9788818 0.61510585
## 19: 0.001864476 -3.0095246 0.9788818 0.61510585
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.003563035 -2.1172717 0.8723685 0.47463144
## 26: 0.001370130 -3.1781458 0.9289840 0.55960768
## 27: 0.001370130 -3.1781458 0.9289840 0.55960768
## 28: 0.001370130 -3.1781458 0.9289840 0.55960768
## 29: 0.001370130 -3.1781458 0.9289840 0.55960768
## 30: 0.001370130 -3.1781458 0.9289840 0.55960768
## 31: 0.001370130 -3.1781458 0.9289840 0.55960768
## 32: 0.001370130 -3.1781458 0.9289840 0.55960768
## 33: 0.001370130 -3.1781458 0.9289840 0.55960768
## 34: 0.005277101 -0.7191323 0.5947468 0.03730409
## 35: 0.005277101 -0.7191323 0.5947468 0.03730409
## 36: 0.005277101 -0.7191323 0.5947468 0.03730409
## 37: 0.005289339 -1.7163469 1.3494170 0.51125155
## 38: 0.005289339 -1.7163469 1.3494170 0.51125155
## 39: 0.005289339 -1.7163469 1.3494170 0.51125155
## 40: 0.005184396 -0.5512413 0.7915023 0.13830228
## 41: 0.005184396 -0.5512413 0.7915023 0.13830228
## 42: 0.005184396 -0.5512413 0.7915023 0.13830228
## 43: 0.005184396 -0.5512413 0.7915023 0.13830228
## 44: 0.005184396 -0.5512413 0.7915023 0.13830228
## 45: 0.005184396 -0.5512413 0.7915023 0.13830228
## 46: 0.005184396 -0.5512413 0.7915023 0.13830228
## 47: 0.005184396 -0.5512413 0.7915023 0.13830228
## 48: 0.005184396 -0.5512413 0.7915023 0.13830228
## 49: 0.005184396 -0.5512413 0.7915023 0.13830228
## 50: 0.005184396 -0.5512413 0.7915023 0.13830228
## 51: 0.005184396 -0.5512413 0.7915023 0.13830228
## 52: 0.005184396 -0.5512413 0.7915023 0.13830228
## 53: 0.005314391 -0.9727072 0.8743440 0.26787994
## 54: 0.005314391 -0.9727072 0.8743440 0.26787994
## 55: 0.005314391 -0.9727072 0.8743440 0.26787994
## 56: 0.005314391 -0.9727072 0.8743440 0.26787994
## 57: 0.005314391 -0.9727072 0.8743440 0.26787994
## 58: 0.005314391 -0.9727072 0.8743440 0.26787994
## 59: 0.005314391 -0.9727072 0.8743440 0.26787994
## 60: 0.005314391 -0.9727072 0.8743440 0.26787994
## 61: 0.005314391 -0.9727072 0.8743440 0.26787994
## 62: 0.005314391 -0.9727072 0.8743440 0.26787994
## 63: 0.005314391 -0.9727072 0.8743440 0.26787994
## 64: 0.005314391 -0.9727072 0.8743440 0.26787994
## 65: 0.005314391 -0.9727072 0.8743440 0.26787994
## 66: 0.005314391 -0.9727072 0.8743440 0.26787994
## 67: 0.005314391 -0.9727072 0.8743440 0.26787994
## 68: 0.005314391 -0.9727072 0.8743440 0.26787994
## 69: 0.005288858 -0.8567880 0.7295011 0.03771967
## 70: 0.005288858 -0.8567880 0.7295011 0.03771967
## 71: 0.005288858 -0.8567880 0.7295011 0.03771967
## 72: 0.005328329 -0.9683955 0.9780811 0.28653102
## 73: 0.005328329 -0.9683955 0.9780811 0.28653102
## 74: 0.004586799 -1.5470381 0.7851831 0.39223675
## 75: 0.004586799 -1.5470381 0.7851831 0.39223675
## 76: 0.005186459 -1.6477916 1.2256298 0.38455221
##           se.bp          v         c       pchi

## [1] "ORF65_1" "ORF62"   "ORF28"   "ORF68"   "ORF76"   "ORF49"
## [1] 6
##  [1] "ORF6"    "ORF18"   "ORF64_1" "ORF12"   "ORF13"   "ORF15"   "ORF16"  
##  [8] "ORF35"   "ORF41"   "ORF48"   "ORF52"   "ORF54"   "ORF57"   "ORF60"  
## [15] "ORF71"   "ORF72"   "ORF24"   "ORF74"   "ORF76"
## [1] 19

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp        se.si        se.au
##       <int>  <char>     <num>     <num>     <num>        <num>        <num>
##  1:       1    ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  2:       1   ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  3:       1   ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  4:       1   ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  5:       1   ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  6:       1   ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  7:       1   ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  8:       1   ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
##  9:       1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10:       1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11:       1  NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12:       2    ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 13:       2    ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 14:       2    ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 15:       2   ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 16:       2   ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 17:       2   ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 18:       2   ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 19:       2   ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 20:       2   ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21:       2   ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22:       2   ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23:       2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24:       2   ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25:       3    ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 26:       4    ORF5 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 27:       4    ORF7 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 28:       4   ORF10 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 29:       4   ORF17 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 30:       4   ORF30 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 31:       4   ORF53 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 32:       4   ORF63 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 33:       4   ORF69 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 34:       5    ORF6 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 35:       5   ORF18 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 36:       5 ORF64_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 37:       6    ORF9 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 38:       6   ORF37 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 39:       6   ORF51 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 40:       7   ORF12 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 41:       7   ORF13 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 42:       7   ORF15 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 43:       7   ORF16 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 44:       7   ORF35 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 45:       7   ORF41 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 46:       7   ORF48 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 47:       7   ORF52 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 48:       7   ORF54 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 49:       7   ORF57 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 50:       7   ORF60 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 51:       7   ORF71 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 52:       7   ORF72 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 53:       8   ORF22 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 54:       8   ORF23 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 55:       8   ORF25 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 56:       8   ORF28 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 57:       8   ORF33 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 58:       8 ORF35.5 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 59:       8   ORF39 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 60:       8     CTO 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 61:       8   ORF42 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 62:       8   ORF43 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 63:       8   ORF44 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 64:       8   ORF46 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 65:       8   ORF58 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 66:       8   ORF62 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 67:       8   ORF68 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 68:       8   ORF75 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 69:       9   ORF24 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 70:       9   ORF74 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 71:       9   ORF76 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 72:      10   ORF27 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 73:      10   ORF32 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 74:      11   ORF49 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 75:      11  NOIR_1 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 76:      12   ORF70 0.9815714 0.9979697 0.6635465 3.593511e-03 5.276070e-04
##     cluster    gene        si        au        bp        se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.001626964 -3.0659483 0.9195982 0.57648065
##  2: 0.001626964 -3.0659483 0.9195982 0.57648065
##  3: 0.001626964 -3.0659483 0.9195982 0.57648065
##  4: 0.001626964 -3.0659483 0.9195982 0.57648065
##  5: 0.001626964 -3.0659483 0.9195982 0.57648065
##  6: 0.001626964 -3.0659483 0.9195982 0.57648065
##  7: 0.001626964 -3.0659483 0.9195982 0.57648065
##  8: 0.001626964 -3.0659483 0.9195982 0.57648065
##  9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001864476 -3.0095246 0.9788818 0.61510585
## 13: 0.001864476 -3.0095246 0.9788818 0.61510585
## 14: 0.001864476 -3.0095246 0.9788818 0.61510585
## 15: 0.001864476 -3.0095246 0.9788818 0.61510585
## 16: 0.001864476 -3.0095246 0.9788818 0.61510585
## 17: 0.001864476 -3.0095246 0.9788818 0.61510585
## 18: 0.001864476 -3.0095246 0.9788818 0.61510585
## 19: 0.001864476 -3.0095246 0.9788818 0.61510585
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.003563035 -2.1172717 0.8723685 0.47463144
## 26: 0.001370130 -3.1781458 0.9289840 0.55960768
## 27: 0.001370130 -3.1781458 0.9289840 0.55960768
## 28: 0.001370130 -3.1781458 0.9289840 0.55960768
## 29: 0.001370130 -3.1781458 0.9289840 0.55960768
## 30: 0.001370130 -3.1781458 0.9289840 0.55960768
## 31: 0.001370130 -3.1781458 0.9289840 0.55960768
## 32: 0.001370130 -3.1781458 0.9289840 0.55960768
## 33: 0.001370130 -3.1781458 0.9289840 0.55960768
## 34: 0.005277101 -0.7191323 0.5947468 0.03730409
## 35: 0.005277101 -0.7191323 0.5947468 0.03730409
## 36: 0.005277101 -0.7191323 0.5947468 0.03730409
## 37: 0.005289339 -1.7163469 1.3494170 0.51125155
## 38: 0.005289339 -1.7163469 1.3494170 0.51125155
## 39: 0.005289339 -1.7163469 1.3494170 0.51125155
## 40: 0.005184396 -0.5512413 0.7915023 0.13830228
## 41: 0.005184396 -0.5512413 0.7915023 0.13830228
## 42: 0.005184396 -0.5512413 0.7915023 0.13830228
## 43: 0.005184396 -0.5512413 0.7915023 0.13830228
## 44: 0.005184396 -0.5512413 0.7915023 0.13830228
## 45: 0.005184396 -0.5512413 0.7915023 0.13830228
## 46: 0.005184396 -0.5512413 0.7915023 0.13830228
## 47: 0.005184396 -0.5512413 0.7915023 0.13830228
## 48: 0.005184396 -0.5512413 0.7915023 0.13830228
## 49: 0.005184396 -0.5512413 0.7915023 0.13830228
## 50: 0.005184396 -0.5512413 0.7915023 0.13830228
## 51: 0.005184396 -0.5512413 0.7915023 0.13830228
## 52: 0.005184396 -0.5512413 0.7915023 0.13830228
## 53: 0.005314391 -0.9727072 0.8743440 0.26787994
## 54: 0.005314391 -0.9727072 0.8743440 0.26787994
## 55: 0.005314391 -0.9727072 0.8743440 0.26787994
## 56: 0.005314391 -0.9727072 0.8743440 0.26787994
## 57: 0.005314391 -0.9727072 0.8743440 0.26787994
## 58: 0.005314391 -0.9727072 0.8743440 0.26787994
## 59: 0.005314391 -0.9727072 0.8743440 0.26787994
## 60: 0.005314391 -0.9727072 0.8743440 0.26787994
## 61: 0.005314391 -0.9727072 0.8743440 0.26787994
## 62: 0.005314391 -0.9727072 0.8743440 0.26787994
## 63: 0.005314391 -0.9727072 0.8743440 0.26787994
## 64: 0.005314391 -0.9727072 0.8743440 0.26787994
## 65: 0.005314391 -0.9727072 0.8743440 0.26787994
## 66: 0.005314391 -0.9727072 0.8743440 0.26787994
## 67: 0.005314391 -0.9727072 0.8743440 0.26787994
## 68: 0.005314391 -0.9727072 0.8743440 0.26787994
## 69: 0.005288858 -0.8567880 0.7295011 0.03771967
## 70: 0.005288858 -0.8567880 0.7295011 0.03771967
## 71: 0.005288858 -0.8567880 0.7295011 0.03771967
## 72: 0.005328329 -0.9683955 0.9780811 0.28653102
## 73: 0.005328329 -0.9683955 0.9780811 0.28653102
## 74: 0.004586799 -1.5470381 0.7851831 0.39223675
## 75: 0.004586799 -1.5470381 0.7851831 0.39223675
## 76: 0.005186459 -1.6477916 1.2256298 0.38455221
##           se.bp          v         c       pchi

## [1] "ORF65_1" "ORF62"   "ORF28"   "ORF68"   "ORF76"   "ORF49"
## [1] 6
##  [1] "ORF6"    "ORF18"   "ORF64_1" "ORF12"   "ORF13"   "ORF15"   "ORF16"  
##  [8] "ORF35"   "ORF41"   "ORF48"   "ORF52"   "ORF54"   "ORF57"   "ORF60"  
## [15] "ORF71"   "ORF72"   "ORF24"   "ORF74"   "ORF76"
## [1] 19

Remove genes from clusters ?

##  [1] "ORF6"    "ORF18"   "ORF64_1" "ORF12"   "ORF13"   "ORF15"   "ORF16"  
##  [8] "ORF35"   "ORF41"   "ORF48"   "ORF52"   "ORF54"   "ORF57"   "ORF60"  
## [15] "ORF71"   "ORF72"   "ORF24"   "ORF74"   "ORF76"
## [1] 19
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       8    16
##  2:       2    13
##  3:       7    13
##  4:       1    11
##  5:       4     8
##  6:       5     3
##  7:       6     3
##  8:       9     3
##  9:      10     2
## 10:      11     2
## 11:       3     1
## 12:      12     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters